It is increasingly recognized that humans and other animals are multi-organismal, comprising co-evolved animal cells and microbial cells. The implications are profound. For example, interactions with pathogens are just a small subset of the diversity of animal-microbial interactions, and human health can only be understood fully in the context of the resident microbiota. This growing appreciation of the ubiquity and importance of beneficial microbes is both contributing to, and builds on, remarkable advances in our capacity to determine the diversity and function of complex microbial communities, especially through advanced sequencing methods. The impacts of this research include a re-evaluation of the nature of animal-microbial interactions and immense opportunities for novel therapies to promote human health. The 2014 Beneficial Microbes Conference will provide a forum for the exchange of the latest conceptual and technological developments in this fast-moving field. It will provide an overview of the current state of research and future directions of inquiry, achieved by bringing together US and international researchers from multiple disciplines (microbiology, immunology, genomics, nutrition, ecology, systems biology, evolutionary biology and clinical science) who study a diversity of associations. Core sponsorship has generously been provided by The American Society for Microbiology (ASM), and the meeting will be held in Washington DC on 27-30 September, 2014. The meeting has five sessions: (1) Beneficial Microbes in Human Health and Disease, to identify the causal roles of microbiota in promoting health and influencing susceptibility to disease (2) Evolutionary Dynamics of Host-Microbe Interactions, especially how coevolution among microbes and between host & microbes can shape host-microbial interactions; (3) Diet and Immune Function: Cross-Species Perspectives, will investigate the role of diet (both nutrition and pre/probiotic formulations) in regulating immunological function, in humans, biomedical models and other systems; (4) The Ecology of Host-Microbial Interactions will apply principles of population ecology and community ecology to explain and predict the composition and function of host-associated microbial communities; and (5) Microbiota and the Gut-Brain Axis will explore the impact of microbiota on brain function and behavior, including feeding, activity and indices of mood. Each session will include two invited talks, four talks selected from submitted abstracts, and a further talk (invited or selected) per session with a quantitative flavor, to disseminate best practice in analysis of large datasets and facilitate discussion of outstanding barriers to computational analysis and mathematical modeling of host-microbial interactions. The conference will include advertised opportunities for break-out groups to discuss specific topics, and a Conference Discussion on Future Directions in Beneficial Microbes Research, which will be the foundation for a published commentary on research priorities to overcome current barriers to advancement of the field. Invitations and travel funds will ensure that early-career researchers, women and minorities are well-represented among speakers and all participants.